Loading Library

library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)

Loading the results of running GSEA on Diabetes dataset

GSEA was separately run and the enrichment results are saved. We upload the results and select the significant findings.

gsea_results <- read.csv("./GSEA diabetes/gsea_diabetes_enrichment_results_v6.2.csv", sep = ",", row.names = 1)
# rownames(gsea_results) <- (rownames(gsea_results)) #tolower removed
gsea_results_significant <- subset(gsea_results, NOM.p.val <0.05 )

Loading the expressions and pathway sets of Diabetes databse

We use the colapsed symbols to genes expression data for expressions. GSEA uses a chip functoin for connecting the uncollapsed to collapsed data. I am currently figuring out how ti perfprms that step. For now not collapsing serves the purpose. Genotypes are 33 mutants and 17 wild types. Pathways are read as done is GSEA. To remain consistent with GSEA we remove the pathways with sizes below 15 and above 500 as well as pathways that have less than 15 genes present in inside the expression matrix.

expressions <- read.csv("./GSEA diabetes/Diabetes_collapsed_symbols_R.csv", sep = ",", row.names = 1)
genotypes <- read.csv("./GSEA diabetes/Diabetes_genotype.txt", sep=" ", header = F)
genotypes <- as.vector(unname(ifelse( genotypes==1,1,0)))
gene_names <- rownames(expressions)
expressions <- expressions[-1]
expressions <- t(expressions)
dim(expressions)
## [1]    34 15056
pathway <- read.csv("./msigdb_v6.2_files_to_download_locally/msigdb_v6.2_GMTs_R/curated gene sets/c2.all.v6.2.symbols.csv", sep = ",", row.names = 1,na.strings = "", colClasses="character")

pathway <- pathway[,-1]
pathway <- t(pathway)
row.names(pathway) <- NULL
pathway <- as.data.frame(pathway)
pathway=lapply(pathway, function(x) x[!is.na(x)] )
pathway=lapply(pathway, function(x) as.character(x))
# pathway_collapsed <- pathway[sapply(pathway,function(x) {(15 <= length(x)) &&(length(x) <= 500)&& sum(colnames(expressions)%in%x)>15})]

pathway_collapsed <- pathway[names(pathway) %in% rownames(gsea_results)]

min(sapply(pathway_collapsed,length))
## [1] 15
individual_pathway_length <- sapply(pathway_collapsed,length)
gene_number <- length(gene_names)
pathway_number <- length(individual_pathway_length)
pathway_number
## [1] 3525

Running Dcor and Univariate ttest over the pathways

Expressions concordant with specific pathways are chosen and dcor and univariate t.test are applied on them. The univariate test is adjusted for FDR correction.

dcor_results <- list()
univariate_results <- list()
univariate_results_adjusted <- list()

for (ii in 1:length(pathway_collapsed)){
pathway_expressions <- expressions[,colnames(expressions)%in% pathway_collapsed[[ii]]]

 dcor_results[ii] <- dcor((pathway_expressions),(genotypes))

}
names(dcor_results)  <- names( pathway_collapsed)

Simulating MPEA Surrogate over the array.

set.seed(0)
# surrogate_dcor <- list()
num_simulation <- 999
cl<-makeCluster(6)
registerDoParallel(cl)

surrogate_dcor <- foreach (ii = 1:pathway_number,  .export = c("num_simulation","gene_number","individual_pathway_length","genotypes"), .packages = "energy") %dopar%{
  if(ii%%100==0) print(ii)
  aux_dcor <- NULL
    for ( jj in 1: num_simulation)
    {
      aux_genes <- sample(1:gene_number,individual_pathway_length[ii])
      aux_dcor[jj] <- dcor(expressions[,aux_genes],genotypes)
    
    }  
  # surrogate_dcor[[ii]] <- aux_dcor
  aux_dcor
}
## Warning in e$fun(obj, substitute(ex), parent.frame(), e$data):
## already exporting variable(s): num_simulation, gene_number,
## individual_pathway_length, genotypes
stopCluster(cl)
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (1+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
##                 KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP 
##                                                 0.001 
##                       HEIDENBLAD_AMPLICON_12P11_12_UP 
##                                                 0.001 
## LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP 
##                                                 0.001 
##                            GROSS_HYPOXIA_VIA_HIF1A_UP 
##                                                 0.001 
##                      MORI_SMALL_PRE_BII_LYMPHOCYTE_UP 
##                                                 0.001 
##                      SHEPARD_CRUSH_AND_BURN_MUTANT_UP 
##                                                 0.001 
##                         MA_MYELOID_DIFFERENTIATION_DN 
##                                                 0.001 
##                      ZHENG_FOXP3_TARGETS_IN_THYMUS_UP 
##                                                 0.001 
##                      LEE_DIFFERENTIATING_T_LYMPHOCYTE 
##                                                 0.001 
##                               WHITFIELD_CELL_CYCLE_G2 
##                                                 0.001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
nominal_dcor_q_values_under_25
## named numeric(0)

Identifying the pathways deemed significant in both GSEA and MPEA

Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))

Mutually_identified_in_GSEA_dcor
##  [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP"
##  [2] "GROSS_HYPOXIA_VIA_HIF1A_UP"                           
##  [3] "REACTOME_MEIOSIS"                                     
##  [4] "REACTOME_CHROMOSOME_MAINTENANCE"                      
##  [5] "REACTOME_MEIOTIC_SYNAPSIS"                            
##  [6] "MORI_IMMATURE_B_LYMPHOCYTE_UP"                        
##  [7] "REACTOME_MRNA_CAPPING"                                
##  [8] "LANDIS_ERBB2_BREAST_TUMORS_65_UP"                     
##  [9] "FERRANDO_TAL1_NEIGHBORS"                              
## [10] "REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER"            
## [11] "SMID_BREAST_CANCER_ERBB2_UP"                          
## [12] "REACTOME_NUCLEOTIDE_EXCISION_REPAIR"                  
## [13] "OHGUCHI_LIVER_HNF4A_TARGETS_UP"                       
## [14] "GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP"                
## [15] "KEGG_HUNTINGTONS_DISEASE"                             
## [16] "PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP"                 
## [17] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"    
## [18] "WONG_MITOCHONDRIA_GENE_MODULE"                        
## [19] "KEGG_OXIDATIVE_PHOSPHORYLATION"                       
## [20] "FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN"                
## [21] "REACTOME_DNA_REPAIR"                                  
## [22] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13"     
## [23] "BIDUS_METASTASIS_DN"                                  
## [24] "MOOTHA_VOXPHOS"

Identifying the pathways significant in MPEA not in GSEA

Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP HEIDENBLAD_AMPLICON_12P11_12_UP MORI_SMALL_PRE_BII_LYMPHOCYTE_UP SHEPARD_CRUSH_AND_BURN_MUTANT_UP MA_MYELOID_DIFFERENTIATION_DN ZHENG_FOXP3_TARGETS_IN_THYMUS_UP LEE_DIFFERENTIATING_T_LYMPHOCYTE WHITFIELD_CELL_CYCLE_G2 CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER SMITH_TERT_TARGETS_DN WANG_TARGETS_OF_MLL_CBP_FUSION_DN ZHANG_TLX_TARGETS_60HR_DN WIERENGA_STAT5A_TARGETS_UP ENK_UV_RESPONSE_KERATINOCYTE_DN FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP FRIDMAN_IMMORTALIZATION_DN GEORGES_TARGETS_OF_MIR192_AND_MIR215 FOSTER_TOLERANT_MACROPHAGE_UP WALLACE_PROSTATE_CANCER_RACE_UP WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP WIERENGA_STAT5A_TARGETS_GROUP1 BHAT_ESR1_TARGETS_VIA_AKT1_UP FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS PID_PTP1B_PATHWAY SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP MITSIADES_RESPONSE_TO_APLIDIN_UP PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN GARY_CD5_TARGETS_DN CAFFAREL_RESPONSE_TO_THC_DN OUILLETTE_CLL_13Q14_DELETION_DN ENGELMANN_CANCER_PROGENITORS_DN REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP KEGG_STEROID_BIOSYNTHESIS KEGG_RNA_POLYMERASE PID_EPHA_FWDPATHWAY JAEGER_METASTASIS_DN LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN BIOCARTA_CARDIACEGF_PATHWAY REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA FORTSCHEGGER_PHF8_TARGETS_UP LIU_PROSTATE_CANCER_UP LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q BROWNE_HCMV_INFECTION_48HR_UP HORTON_SREBF_TARGETS BIOCARTA_PAR1_PATHWAY REACTOME_MICRORNA_MIRNA_BIOGENESIS REACTOME_PI3K_AKT_ACTIVATION REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX BORCZUK_MALIGNANT_MESOTHELIOMA_UP REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX NAGASHIMA_NRG1_SIGNALING_DN CHEBOTAEV_GR_TARGETS_DN GEISS_RESPONSE_TO_DSRNA_DN LABBE_WNT3A_TARGETS_DN HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS KEGG_PYRIMIDINE_METABOLISM FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL MACLACHLAN_BRCA1_TARGETS_UP QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 PID_S1P_S1P2_PATHWAY YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN PID_LIS1_PATHWAY REACTOME_REGULATORY_RNA_PATHWAYS REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE SHI_SPARC_TARGETS_UP ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP PLASARI_NFIC_TARGETS_BASAL_UP PID_PRL_SIGNALING_EVENTS_PATHWAY PID_S1P_S1P3_PATHWAY PID_EPHA2_FWD_PATHWAY HOUSTIS_ROS ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN PID_AVB3_INTEGRIN_PATHWAY DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP SANSOM_APC_TARGETS_DN RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP PID_ECADHERIN_KERATINOCYTE_PATHWAY REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING PETROVA_PROX1_TARGETS_UP BROWNE_HCMV_INFECTION_6HR_DN CHEN_ETV5_TARGETS_TESTIS NADLER_HYPERGLYCEMIA_AT_OBESITY DAZARD_RESPONSE_TO_UV_NHEK_DN WINNEPENNINCKX_MELANOMA_METASTASIS_DN BIOCARTA_CDC42RAC_PATHWAY PID_P53_REGULATION_PATHWAY GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN MULLIGHAN_NPM1_SIGNATURE_3_UP SHEN_SMARCA2_TARGETS_UP SA_TRKA_RECEPTOR PID_TGFBR_PATHWAY REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING PETRETTO_CARDIAC_HYPERTROPHY ONDER_CDH1_TARGETS_1_UP BILD_MYC_ONCOGENIC_SIGNATURE RIGGI_EWING_SARCOMA_PROGENITOR_DN PID_WNT_NONCANONICAL_PATHWAY GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN VERHAAK_GLIOBLASTOMA_NEURAL KASLER_HDAC7_TARGETS_1_DN PID_S1P_S1P1_PATHWAY TARTE_PLASMA_CELL_VS_PLASMABLAST_DN MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN PLASARI_TGFB1_TARGETS_10HR_DN REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION MENSE_HYPOXIA_UP BOCHKIS_FOXA2_TARGETS BIOCARTA_RAS_PATHWAY PID_SYNDECAN_4_PATHWAY REACTOME_RNA_POL_III_TRANSCRIPTION MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN GAJATE_RESPONSE_TO_TRABECTEDIN_UP MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 COATES_MACROPHAGE_M1_VS_M2_DN LIN_NPAS4_TARGETS_UP REACTOME_G_ALPHA1213_SIGNALLING_EVENTS FARMER_BREAST_CANCER_APOCRINE_VS_BASAL JOHNSTONE_PARVB_TARGETS_3_UP KENNY_CTNNB1_TARGETS_DN BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP WANG_SMARCE1_TARGETS_UP LEIN_CHOROID_PLEXUS_MARKERS BERNARD_PPAPDC1B_TARGETS_UP BROWNE_HCMV_INFECTION_4HR_DN MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN HU_ANGIOGENESIS_DN SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY NUYTTEN_NIPP1_TARGETS_UP SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP MURAKAMI_UV_RESPONSE_6HR_DN BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS WIERENGA_STAT5A_TARGETS_GROUP2 CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP BASAKI_YBX1_TARGETS_UP RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP LENAOUR_DENDRITIC_CELL_MATURATION_DN WINZEN_DEGRADED_VIA_KHSRP LIU_SOX4_TARGETS_UP PENG_RAPAMYCIN_RESPONSE_UP ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP BIOCARTA_EDG1_PATHWAY PID_ECADHERIN_NASCENT_AJ_PATHWAY NOJIMA_SFRP2_TARGETS_UP ODONNELL_METASTASIS_DN LEE_TARGETS_OF_PTCH1_AND_SUFU_DN UEDA_PERIFERAL_CLOCK HASLINGER_B_CLL_WITH_MUTATED_VH_GENES MCCLUNG_COCAINE_REWARD_5D CADWELL_ATG16L1_TARGETS_DN MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED LI_INDUCED_T_TO_NATURAL_KILLER_DN GUILLAUMOND_KLF10_TARGETS_DN BIOCARTA_PTDINS_PATHWAY SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN MARKS_HDAC_TARGETS_UP VANTVEER_BREAST_CANCER_ESR1_UP GUTIERREZ_MULTIPLE_MYELOMA_UP REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE REACTOME_CHOLESTEROL_BIOSYNTHESIS ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP RODWELL_AGING_KIDNEY_NO_BLOOD_DN AMIT_EGF_RESPONSE_40_MCF10A SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER MOREIRA_RESPONSE_TO_TSA_UP MURAKAMI_UV_RESPONSE_24HR YAMASHITA_METHYLATED_IN_PROSTATE_CANCER FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP GOLUB_ALL_VS_AML_DN MASSARWEH_RESPONSE_TO_ESTRADIOL BRUECKNER_TARGETS_OF_MIRLET7A3_UP REACTOME_PEROXISOMAL_LIPID_METABOLISM REACTOME_MRNA_SPLICING_MINOR_PATHWAY VARELA_ZMPSTE24_TARGETS_UP DE_YY1_TARGETS_UP TIAN_TNF_SIGNALING_NOT_VIA_NFKB HUANG_GATA2_TARGETS_UP KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP PUJANA_BRCA2_PCC_NETWORK RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN CUI_GLUCOSE_DEPRIVATION BIOCARTA_RACCYCD_PATHWAY GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN KEEN_RESPONSE_TO_ROSIGLITAZONE_UP BURTON_ADIPOGENESIS_6 COATES_MACROPHAGE_M1_VS_M2_UP MANALO_HYPOXIA_DN VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING MISSIAGLIA_REGULATED_BY_METHYLATION_UP SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP BIOCARTA_P53HYPOXIA_PATHWAY PID_IL4_2PATHWAY YAGI_AML_RELAPSE_PROGNOSIS HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP RICKMAN_METASTASIS_UP CUI_TCF21_TARGETS_DN YAGI_AML_WITH_T_8_21_TRANSLOCATION WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP TERAMOTO_OPN_TARGETS_CLUSTER_7 PETRETTO_HEART_MASS_QTL_CIS_DN LAMB_CCND1_TARGETS GENTILE_UV_LOW_DOSE_UP
MPEA 0.0010 0.0010 0.0010 0.0010 0.0010 0.0010 0.0010 0.0010 0.0020 0.002 0.0020 0.0020 0.0020 0.0020 0.0020 0.0030 0.0030 0.0040 0.0040 0.0040 0.0040 0.0040 0.0050 0.005 0.005 0.0050 0.0060 0.0060 0.0060 0.006 0.0060 0.0070 0.0070 0.0070 0.0070 0.008 0.0080 0.0080 0.0080 0.0090 0.0090 0.009 0.0090 0.0090 0.0090 0.0100 0.0100 0.0100 0.0110 0.0110 0.0110 0.0110 0.0120 0.0120 0.012 0.0120 0.0120 0.0130 0.0130 0.0130 0.0130 0.0130 0.0130 0.0140 0.014 0.0140 0.0140 0.0150 0.0150 0.0160 0.0160 0.017 0.0170 0.0170 0.0170 0.0170 0.0170 0.017 0.0170 0.018 0.0180 0.018 0.0180 0.0180 0.019 0.0190 0.0190 0.0190 0.0200 0.0200 0.0200 0.0200 0.0200 0.0210 0.0210 0.0210 0.0220 0.0220 0.0220 0.0220 0.0220 0.023 0.023 0.0230 0.023 0.0230 0.0230 0.023 0.0240 0.0240 0.0240 0.0240 0.0250 0.0250 0.0250 0.0250 0.0260 0.0260 0.0260 0.0280 0.0280 0.0280 0.0280 0.0280 0.0280 0.0280 0.0280 0.0280 0.0280 0.0290 0.0290 0.0290 0.0300 0.0300 0.0300 0.0300 0.0300 0.0300 0.0310 0.0310 0.0310 0.031 0.0310 0.0310 0.0310 0.031 0.0310 0.0320 0.0320 0.032 0.0320 0.0320 0.0320 0.0330 0.0330 0.033 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.0340 0.034 0.0350 0.0350 0.0350 0.0350 0.0350 0.0360 0.0360 0.0360 0.0360 0.0370 0.0370 0.0380 0.0380 0.0380 0.0380 0.0380 0.0390 0.0390 0.0390 0.040 0.0400 0.0400 0.0400 0.0400 0.0400 0.041 0.0410 0.0410 0.0410 0.0410 0.0410 0.042 0.042 0.0420 0.0420 0.0420 0.0430 0.0430 0.0430 0.0430 0.044 0.045 0.0450 0.0450 0.0450 0.0470 0.0470 0.0470 0.0470 0.0470 0.048 0.0480 0.0480 0.0480 0.0490 0.0490 0.0490 0.0490 0.0490
GSEA 0.7939 0.5246 0.5202 0.1169 0.2189 0.8133 0.7427 0.9876 0.2354 0.632 0.4907 0.3854 0.7294 0.1515 0.2618 0.6447 0.7864 0.1394 0.7462 0.2096 0.3752 0.7976 0.2458 0.247 0.741 0.6335 0.9792 0.2016 0.0977 0.497 0.5279 0.3593 0.7019 0.1467 0.7563 0.373 0.5545 0.9084 0.8959 0.1972 0.3138 0.302 0.8517 0.2785 0.1566 0.4626 0.2172 0.6378 0.1481 0.0638 0.4706 0.6083 0.2609 0.4038 0.917 0.1454 0.8423 0.0541 0.1127 0.2548 0.0813 0.4839 0.9648 0.3037 0.703 0.5885 0.6437 0.2688 0.3533 0.7234 0.7505 0.384 0.4038 0.0671 0.6747 0.9248 0.4812 0.175 0.4008 0.256 0.9014 0.211 0.2281 0.6826 0.996 0.8059 0.8822 0.4369 0.3123 0.1959 0.7256 0.0855 0.5264 0.7196 0.5838 0.7666 0.7375 0.3551 0.4255 0.3267 0.8546 0.854 0.782 0.9123 0.880 0.7146 0.8869 1.000 0.4346 0.1713 0.3777 0.7206 0.3119 0.6093 0.2385 0.9283 0.0601 0.2758 0.2924 0.9403 0.5322 0.7442 0.5078 0.8377 0.6223 0.3733 0.7515 0.6968 0.5515 0.0881 0.9593 0.8516 0.4942 0.4124 0.5445 0.9053 0.6982 0.6963 0.6245 0.0678 0.1904 0.089 0.2358 0.7084 0.7202 0.666 0.6593 0.9772 0.4047 0.876 0.3984 0.7992 0.6371 0.4286 0.7784 0.384 0.8806 0.3631 0.2772 0.4688 0.2615 0.9724 0.0972 0.8103 0.6754 0.6888 0.2965 0.368 0.8613 0.4838 0.7025 0.7947 0.8244 0.6598 0.5293 0.2464 0.0569 0.0754 0.5215 0.5219 0.6068 0.3401 0.5592 0.4038 0.2063 0.2093 0.6701 0.292 0.1794 0.9941 0.1357 0.2604 0.4879 0.246 0.7146 0.4928 0.8337 0.8665 0.2231 0.625 0.383 0.7918 0.1412 0.4199 0.5386 0.4118 0.3041 0.5193 0.623 0.657 0.1187 0.1116 0.4714 0.0547 0.8487 0.7898 0.6578 0.5984 0.349 0.4052 0.6274 0.8939 0.3212 0.5247 0.1475 0.8735 0.5937

Identifying the pathways significant in GSEA not in MPEA

Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
LUI_TARGETS_OF_PAX8_PPARG_FUSION LUI_THYROID_CANCER_CLUSTER_3 ANDERSEN_LIVER_CANCER_KRT19_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN MCBRYAN_PUBERTAL_BREAST_3_4WK_DN REACTOME_INFLUENZA_LIFE_CYCLE LANDIS_ERBB2_BREAST_TUMORS_324_UP KEGG_ALZHEIMERS_DISEASE REACTOME_METABOLISM_OF_RNA CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY REACTOME_METABOLISM_OF_MRNA PECE_MAMMARY_STEM_CELL_UP KEGG_NUCLEOTIDE_EXCISION_REPAIR TONG_INTERACT_WITH_PTTG1 EHLERS_ANEUPLOIDY_UP YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP KANNAN_TP53_TARGETS_DN DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_TRANSLATION REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES TAKAO_RESPONSE_TO_UVB_RADIATION_UP BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE HUMMERICH_BENIGN_SKIN_TUMOR_UP HSIAO_HOUSEKEEPING_GENES JAZAG_TGFB1_SIGNALING_UP BAE_BRCA1_TARGETS_UP KEGG_RIBOSOME NUTT_GBM_VS_AO_GLIOMA_DN MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN REACTOME_METABOLISM_OF_PROTEINS BILANGES_SERUM_RESPONSE_TRANSLATION LANDIS_BREAST_CANCER_PROGRESSION_UP NAKAYAMA_FGF2_TARGETS HUNSBERGER_EXERCISE_REGULATED_GENES LUI_THYROID_CANCER_PAX8_PPARG_DN WENG_POR_TARGETS_GLOBAL_UP REACTOME_PEPTIDE_CHAIN_ELONGATION NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON IRITANI_MAD1_TARGETS_DN YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 LEE_LIVER_CANCER_SURVIVAL_DN REACTOME_SIGNAL_AMPLIFICATION WANG_RESPONSE_TO_FORSKOLIN_UP JIANG_AGING_HYPOTHALAMUS_UP PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP KEGG_BASAL_TRANSCRIPTION_FACTORS OSMAN_BLADDER_CANCER_DN YANG_BREAST_CANCER_ESR1_UP ZHAN_MULTIPLE_MYELOMA_HP_UP PARK_HSC_MARKERS REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS WANG_TUMOR_INVASIVENESS_UP REACTOME_GLOBAL_GENOMIC_NER_GG_NER GEORGES_CELL_CYCLE_MIR192_TARGETS MAINA_VHL_TARGETS_DN CHEN_PDGF_TARGETS SCHRAMM_INHBA_TARGETS_DN FAELT_B_CLL_WITH_VH3_21_DN BOUDOUKHA_BOUND_BY_IGF2BP2 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN MURAKAMI_UV_RESPONSE_1HR_UP PID_PI3K_PLC_TRK_PATHWAY REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP CHANGOLKAR_H2AFY_TARGETS_UP BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN BORLAK_LIVER_CANCER_EGF_UP REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 KIM_MYC_AMPLIFICATION_TARGETS_UP LINDGREN_BLADDER_CANCER_CLUSTER_1_UP CHANGOLKAR_H2AFY_TARGETS_DN HORIUCHI_WTAP_TARGETS_DN SASAKI_ADULT_T_CELL_LEUKEMIA GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN REACTOME_INTEGRATION_OF_ENERGY_METABOLISM DELASERNA_MYOD_TARGETS_UP KASLER_HDAC7_TARGETS_2_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN SHIN_B_CELL_LYMPHOMA_CLUSTER_8 DOANE_BREAST_CANCER_ESR1_DN BIOCARTA_AGR_PATHWAY REACTOME_RNA_POL_I_PROMOTER_OPENING REACTOME_HDL_MEDIATED_LIPID_TRANSPORT FAELT_B_CLL_WITH_VH3_21_UP KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 HASLINGER_B_CLL_WITH_6Q21_DELETION KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN KEGG_PPAR_SIGNALING_PATHWAY REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE MIKKELSEN_MEF_LCP_WITH_H3K27ME3 XU_GH1_EXOGENOUS_TARGETS_DN ABE_VEGFA_TARGETS_2HR FIGUEROA_AML_METHYLATION_CLUSTER_1_DN REACTOME_LIPOPROTEIN_METABOLISM BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN BIOCARTA_UCALPAIN_PATHWAY ST_T_CELL_SIGNAL_TRANSDUCTION DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY HUMMERICH_MALIGNANT_SKIN_TUMOR_DN CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP PID_NCADHERIN_PATHWAY HUMMERICH_BENIGN_SKIN_TUMOR_DN REACTOME_PACKAGING_OF_TELOMERE_ENDS LEI_HOXC8_TARGETS_DN PID_BARD1_PATHWAY FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP BIOCARTA_MAL_PATHWAY XU_AKT1_TARGETS_6HR PID_INSULIN_GLUCOSE_PATHWAY REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS SA_B_CELL_RECEPTOR_COMPLEXES SCHEIDEREIT_IKK_INTERACTING_PROTEINS REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP RIZ_ERYTHROID_DIFFERENTIATION_HEMGN MEISSNER_BRAIN_HCP_WITH_H3K27ME3 REACTOME_SEMAPHORIN_INTERACTIONS KUMAR_AUTOPHAGY_NETWORK SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN KENNY_CTNNB1_TARGETS_UP OXFORD_RALA_OR_RALB_TARGETS_UP LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP MIKKELSEN_NPC_HCP_WITH_H3K27ME3 BIOCARTA_HER2_PATHWAY FIGUEROA_AML_METHYLATION_CLUSTER_3_DN KYNG_DNA_DAMAGE_BY_4NQO MULLIGHAN_NPM1_SIGNATURE_3_DN PID_IL23_PATHWAY REACTOME_MEIOTIC_RECOMBINATION MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP QI_HYPOXIA
MPEA 0.325 0.283 0.713 0.0520 0.419 0.2990 0.6250 0.118 0.0780 0.6150 0.5100 0.0730 0.3400 0.212 0.6370 0.6340 0.1550 0.7290 0.4960 0.7090 0.6040 0.4850 0.165 0.6160 0.6400 0.8390 0.169 0.1780 0.6730 0.1910 0.6410 0.278 0.1020 0.6720 0.4620 0.2720 0.5370 0.4930 0.4820 0.8820 0.0670 0.8660 0.3520 0.6730 0.6540 0.4560 0.1790 0.1190 0.5050 0.4040 0.2130 0.7620 0.1650 0.3790 0.253 0.524 0.7410 0.5050 0.6830 0.1370 0.4240 0.1030 0.2840 0.1630 0.091 0.1440 0.0830 0.3890 0.7050 0.144 0.0850 0.1600 0.8210 0.4650 0.6490 0.2340 0.0910 0.4060 0.2480 0.5060 0.4600 0.1790 0.3670 0.936 0.1680 0.1920 0.6280 0.2920 0.933 0.3640 0.783 0.655 0.611 0.9790 0.5370 0.062 0.625 0.329 0.954 0.9900 0.231 0.9180 0.9930 0.5700 0.581 0.4930 0.1740 0.7820 0.9600 0.0960 0.6210 0.8220 0.939 0.9820 0.8330 0.9690 0.5840 0.6320 0.9130 0.9690 0.949 0.191 0.5150 0.6070 0.9460 0.5350 0.8790 0.5360 0.9220 0.4710 0.1050 0.8080 0.6470 0.0770 0.3900 0.9130 0.2370 0.1440 0.5360 0.0700 0.8150 0.1750 0.4160 0.2910 0.2450 0.6140
GSEA 0.002 0.004 0.004 0.0177 0.002 0.0019 0.0158 0.000 0.0121 0.0198 0.0199 0.0141 0.0061 0.010 0.0355 0.0326 0.0115 0.0219 0.0161 0.0256 0.0124 0.0166 0.002 0.0321 0.0325 0.0059 0.014 0.0082 0.0383 0.0123 0.0238 0.000 0.0219 0.0378 0.0339 0.0125 0.0208 0.0374 0.0429 0.0281 0.0337 0.0185 0.0243 0.0161 0.0383 0.0197 0.0178 0.0378 0.0098 0.0168 0.0429 0.0435 0.0329 0.0367 0.025 0.040 0.0382 0.0339 0.0333 0.0468 0.0232 0.0408 0.0376 0.0391 0.038 0.0193 0.0441 0.0376 0.0437 0.047 0.0041 0.0443 0.0444 0.0406 0.0279 0.0409 0.0449 0.0478 0.0361 0.0406 0.0359 0.0231 0.0319 0.041 0.0062 0.0125 0.0161 0.0384 0.000 0.0038 0.002 0.002 0.000 0.0019 0.0061 0.006 0.004 0.000 0.008 0.0082 0.002 0.0041 0.0061 0.0061 0.004 0.0059 0.0348 0.0249 0.0277 0.0138 0.0142 0.0292 0.040 0.0193 0.0488 0.0307 0.0277 0.0357 0.0309 0.0408 0.048 0.046 0.0248 0.0472 0.0198 0.0202 0.0233 0.0435 0.0442 0.0239 0.0449 0.0253 0.0335 0.0431 0.0337 0.0422 0.0081 0.0498 0.0313 0.0364 0.0385 0.0452 0.0475 0.0167 0.0485 0.0354

Univariate Significance analysis on single pathway gene by gene Significant in MPEA and not in GSEA

enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_dcor_not_in_GSEA) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_dcor_not_in_GSEA[[ii]]]],colnames(expressions))
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor

aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}

enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_dcor_not_in_GSEA

enrichment_ratio_comparison%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP HEIDENBLAD_AMPLICON_12P11_12_UP MORI_SMALL_PRE_BII_LYMPHOCYTE_UP SHEPARD_CRUSH_AND_BURN_MUTANT_UP MA_MYELOID_DIFFERENTIATION_DN ZHENG_FOXP3_TARGETS_IN_THYMUS_UP LEE_DIFFERENTIATING_T_LYMPHOCYTE WHITFIELD_CELL_CYCLE_G2 CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER SMITH_TERT_TARGETS_DN WANG_TARGETS_OF_MLL_CBP_FUSION_DN ZHANG_TLX_TARGETS_60HR_DN WIERENGA_STAT5A_TARGETS_UP ENK_UV_RESPONSE_KERATINOCYTE_DN FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP FRIDMAN_IMMORTALIZATION_DN GEORGES_TARGETS_OF_MIR192_AND_MIR215 FOSTER_TOLERANT_MACROPHAGE_UP WALLACE_PROSTATE_CANCER_RACE_UP WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP WIERENGA_STAT5A_TARGETS_GROUP1 BHAT_ESR1_TARGETS_VIA_AKT1_UP FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS PID_PTP1B_PATHWAY SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP MITSIADES_RESPONSE_TO_APLIDIN_UP PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN GARY_CD5_TARGETS_DN CAFFAREL_RESPONSE_TO_THC_DN OUILLETTE_CLL_13Q14_DELETION_DN ENGELMANN_CANCER_PROGENITORS_DN REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP KEGG_STEROID_BIOSYNTHESIS KEGG_RNA_POLYMERASE PID_EPHA_FWDPATHWAY JAEGER_METASTASIS_DN LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN BIOCARTA_CARDIACEGF_PATHWAY REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA FORTSCHEGGER_PHF8_TARGETS_UP LIU_PROSTATE_CANCER_UP LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q BROWNE_HCMV_INFECTION_48HR_UP HORTON_SREBF_TARGETS BIOCARTA_PAR1_PATHWAY REACTOME_MICRORNA_MIRNA_BIOGENESIS REACTOME_PI3K_AKT_ACTIVATION REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX BORCZUK_MALIGNANT_MESOTHELIOMA_UP REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX NAGASHIMA_NRG1_SIGNALING_DN CHEBOTAEV_GR_TARGETS_DN GEISS_RESPONSE_TO_DSRNA_DN LABBE_WNT3A_TARGETS_DN HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS KEGG_PYRIMIDINE_METABOLISM FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL MACLACHLAN_BRCA1_TARGETS_UP QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 PID_S1P_S1P2_PATHWAY YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN PID_LIS1_PATHWAY REACTOME_REGULATORY_RNA_PATHWAYS REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE SHI_SPARC_TARGETS_UP ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP PLASARI_NFIC_TARGETS_BASAL_UP PID_PRL_SIGNALING_EVENTS_PATHWAY PID_S1P_S1P3_PATHWAY PID_EPHA2_FWD_PATHWAY HOUSTIS_ROS ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN PID_AVB3_INTEGRIN_PATHWAY DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP SANSOM_APC_TARGETS_DN RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP PID_ECADHERIN_KERATINOCYTE_PATHWAY REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING PETROVA_PROX1_TARGETS_UP BROWNE_HCMV_INFECTION_6HR_DN CHEN_ETV5_TARGETS_TESTIS NADLER_HYPERGLYCEMIA_AT_OBESITY DAZARD_RESPONSE_TO_UV_NHEK_DN WINNEPENNINCKX_MELANOMA_METASTASIS_DN BIOCARTA_CDC42RAC_PATHWAY PID_P53_REGULATION_PATHWAY GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN MULLIGHAN_NPM1_SIGNATURE_3_UP SHEN_SMARCA2_TARGETS_UP SA_TRKA_RECEPTOR PID_TGFBR_PATHWAY REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING PETRETTO_CARDIAC_HYPERTROPHY ONDER_CDH1_TARGETS_1_UP BILD_MYC_ONCOGENIC_SIGNATURE RIGGI_EWING_SARCOMA_PROGENITOR_DN PID_WNT_NONCANONICAL_PATHWAY GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN VERHAAK_GLIOBLASTOMA_NEURAL KASLER_HDAC7_TARGETS_1_DN PID_S1P_S1P1_PATHWAY TARTE_PLASMA_CELL_VS_PLASMABLAST_DN MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN PLASARI_TGFB1_TARGETS_10HR_DN REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION MENSE_HYPOXIA_UP BOCHKIS_FOXA2_TARGETS BIOCARTA_RAS_PATHWAY PID_SYNDECAN_4_PATHWAY REACTOME_RNA_POL_III_TRANSCRIPTION MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN GAJATE_RESPONSE_TO_TRABECTEDIN_UP MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 COATES_MACROPHAGE_M1_VS_M2_DN LIN_NPAS4_TARGETS_UP REACTOME_G_ALPHA1213_SIGNALLING_EVENTS FARMER_BREAST_CANCER_APOCRINE_VS_BASAL JOHNSTONE_PARVB_TARGETS_3_UP KENNY_CTNNB1_TARGETS_DN BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP WANG_SMARCE1_TARGETS_UP LEIN_CHOROID_PLEXUS_MARKERS BERNARD_PPAPDC1B_TARGETS_UP BROWNE_HCMV_INFECTION_4HR_DN MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN HU_ANGIOGENESIS_DN SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY NUYTTEN_NIPP1_TARGETS_UP SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP MURAKAMI_UV_RESPONSE_6HR_DN BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS WIERENGA_STAT5A_TARGETS_GROUP2 CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP BASAKI_YBX1_TARGETS_UP RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP LENAOUR_DENDRITIC_CELL_MATURATION_DN WINZEN_DEGRADED_VIA_KHSRP LIU_SOX4_TARGETS_UP PENG_RAPAMYCIN_RESPONSE_UP ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP BIOCARTA_EDG1_PATHWAY PID_ECADHERIN_NASCENT_AJ_PATHWAY NOJIMA_SFRP2_TARGETS_UP ODONNELL_METASTASIS_DN LEE_TARGETS_OF_PTCH1_AND_SUFU_DN UEDA_PERIFERAL_CLOCK HASLINGER_B_CLL_WITH_MUTATED_VH_GENES MCCLUNG_COCAINE_REWARD_5D CADWELL_ATG16L1_TARGETS_DN MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED LI_INDUCED_T_TO_NATURAL_KILLER_DN GUILLAUMOND_KLF10_TARGETS_DN BIOCARTA_PTDINS_PATHWAY SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN MARKS_HDAC_TARGETS_UP VANTVEER_BREAST_CANCER_ESR1_UP GUTIERREZ_MULTIPLE_MYELOMA_UP REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE REACTOME_CHOLESTEROL_BIOSYNTHESIS ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP RODWELL_AGING_KIDNEY_NO_BLOOD_DN AMIT_EGF_RESPONSE_40_MCF10A SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER MOREIRA_RESPONSE_TO_TSA_UP MURAKAMI_UV_RESPONSE_24HR YAMASHITA_METHYLATED_IN_PROSTATE_CANCER FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP GOLUB_ALL_VS_AML_DN MASSARWEH_RESPONSE_TO_ESTRADIOL BRUECKNER_TARGETS_OF_MIRLET7A3_UP REACTOME_PEROXISOMAL_LIPID_METABOLISM REACTOME_MRNA_SPLICING_MINOR_PATHWAY VARELA_ZMPSTE24_TARGETS_UP DE_YY1_TARGETS_UP TIAN_TNF_SIGNALING_NOT_VIA_NFKB HUANG_GATA2_TARGETS_UP KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP PUJANA_BRCA2_PCC_NETWORK RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN CUI_GLUCOSE_DEPRIVATION BIOCARTA_RACCYCD_PATHWAY GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN KEEN_RESPONSE_TO_ROSIGLITAZONE_UP BURTON_ADIPOGENESIS_6 COATES_MACROPHAGE_M1_VS_M2_UP MANALO_HYPOXIA_DN VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING MISSIAGLIA_REGULATED_BY_METHYLATION_UP SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP BIOCARTA_P53HYPOXIA_PATHWAY PID_IL4_2PATHWAY YAGI_AML_RELAPSE_PROGNOSIS HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP RICKMAN_METASTASIS_UP CUI_TCF21_TARGETS_DN YAGI_AML_WITH_T_8_21_TRANSLOCATION WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP TERAMOTO_OPN_TARGETS_CLUSTER_7 PETRETTO_HEART_MASS_QTL_CIS_DN LAMB_CCND1_TARGETS GENTILE_UV_LOW_DOSE_UP
MPEA 0.0826 0.0435 0.0968 0.064 0.0556 0.0310 0.0840 0.0294 0.0526 0.0541 0.0526 0.08 0.0667 0.0287 0.0365 0.0249 0.0504 0.0532 0.0645 0.0563 0.0566 0.0377 0.2000 0.0366 0.0517 0.0588 0.04 0.0581 0.0625 0.0437 0.0669 0.0361 0.0455 0.0513 0.0851 0.0870 0.0952 0.0476 0.0403 0.0625 0.1364 0.0667 0.0359 0.1333 0.0435 0.0588 0.05 0.0645 0.0667 0.0759 0.0327 0.0455 0.0571 0.10 0.0385 0.1250 0.0363 0.1481 0.150 0.0571 0.125 0.0649 0.0469 0.0541 0.0474 0.0588 0.0357 0.0909 0.12 0.0263 0.0386 0.12 0.10 0.1026 0.0333 0.0556 0.0217 0.0422 0.0952 0.1 0.0833 0.0588 0.0909 0.0263 0.0725 0.0398 0.0445 0.10 0.0526 0.087 0.087 0.0703 0.0556 0.0851 0.0302 0.0323 0.0625 0.0417 0.0278 0.0397 0.0390 0.0625 0.0408 0.0741 0.1034 0.0467 0.0256 0.0385 0.0357 0.0441 0.0654 0.1250 0.1053 0.0532 0.0385 0.0529 0.0625 0.0333 0.0648 0.0455 0.0333 0.0667 0.0296 0.0303 0.1111 0.1404 0.0476 0.02 0.1011 0.0492 0.0498 0.0569 0.0526 0.0526 0.0506 0.0429 0.0769 0.0343 0.1000 0.0938 0.1923 0.044 0.0633 0 0.0476 0.0556 0.0488 0.037 0.0309 0.0705 0.0645 0.0727 0.026 0.0421 0.0366 0.0469 0.0833 0.1351 0.0417 0.05 0.0508 0.0265 0.2353 0.0615 0.0732 0.0323 0.0875 0.0435 0.0455 0.0435 0.0526 0.0306 0.1034 0.087 0.05 0.0357 0.1010 0.0625 0.1786 0.05 0.1250 0.0556 0.0227 0.08 0.0556 0.0217 0.0267 0.125 0.0606 0.0312 0.1765 0.1053 0.1089 0.04 0.087 0.0172 0.0324 0.03 0.0612 0.0385 0.0238 0.08 0.0676 0.0612 0.0448 0.1176 0.0448 0.046 0.0455 0.0404 0.1351 0.2174 0.0455 0.0476 0.0345 0.069 0.087 0.0769 0.0909 0.0398 0.0909 0.0435 0.0854 0.0000 0.1250 0.0588 0.1053
GSEA 0.0642 0.0435 0.0806 0.048 0.0278 0.0388 0.0756 0.0392 0.1053 0.0473 0.0526 0.08 0.0667 0.0287 0.0438 0.0174 0.0570 0.0560 0.0645 0.0563 0.0660 0.0335 0.1333 0.0488 0.0460 0.0535 0.08 0.0465 0.0565 0.0397 0.0544 0.0289 0.0455 0.0513 0.0426 0.0435 0.0952 0.0381 0.0484 0.1250 0.0909 0.0667 0.0448 0.1000 0.0478 0.0588 0.10 0.0452 0.0833 0.0633 0.0261 0.0455 0.0857 0.05 0.0385 0.0938 0.0403 0.1111 0.125 0.0571 0.125 0.0779 0.0312 0.0405 0.0553 0.0588 0.0357 0.1364 0.12 0.0263 0.0429 0.08 0.05 0.1026 0.0333 0.0556 0.0652 0.0422 0.0476 0.1 0.1250 0.0588 0.0909 0.0789 0.0725 0.0398 0.0582 0.05 0.0526 0.087 0.087 0.0703 0.0556 0.0638 0.0345 0.0645 0.0625 0.0417 0.1111 0.0556 0.0496 0.0625 0.0204 0.0741 0.0345 0.0374 0.0342 0.0385 0.0714 0.0588 0.0374 0.0625 0.1053 0.0456 0.0769 0.0471 0.0625 0.0167 0.0648 0.0455 0.0333 0.0667 0.0443 0.0404 0.1389 0.1053 0.0476 0.02 0.0674 0.0656 0.0536 0.0569 0.0526 0.0526 0.0337 0.0429 0.0385 0.0294 0.0833 0.0625 0.0769 0.044 0.0367 0 0.0476 0.1111 0.0488 0.037 0.0309 0.0601 0.0323 0.0545 0.013 0.0421 0.0427 0.0469 0.0417 0.1081 0.0833 0.10 0.0508 0.0265 0.1765 0.0462 0.0732 0.0323 0.0875 0.0435 0.0455 0.0435 0.0526 0.0306 0.1034 0.087 0.10 0.1071 0.0707 0.0625 0.1071 0.05 0.0833 0.0000 0.1136 0.12 0.1667 0.0217 0.0267 0.125 0.0303 0.0312 0.1765 0.1053 0.0891 0.08 0.087 0.0345 0.0295 0.04 0.0612 0.0385 0.0357 0.08 0.0608 0.0816 0.0448 0.1373 0.0420 0.046 0.0606 0.0303 0.0811 0.1739 0.0909 0.0476 0.0517 0.069 0.087 0.0769 0.0909 0.0284 0.0909 0.0401 0.0610 0.0588 0.1875 0.0588 0.0526 
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
## 
##  Welch Two Sample t-test
## 
## data:  enrichment_ratio_dcor and enrichment_ratio_ttest
## t = 0.44538, df = 444.32, p-value = 0.6563
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -0.004944176  0.007841671
## sample estimates:
##  mean of x  mean of y 
## 0.06485219 0.06340344
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"

enrichment_ratios_percenages%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
Percentage
More univariate enrichment detected in Dcor 33.4802
More univariate enrichment detected in T-test 25.9912
Draw 40.5286

Univariate Significance analysis on single pathway gene by gene Significant in GSEA and not in MPEA

enrichment_ratio_dcor <- NULL
enrichment_ratio_ttest <- NULL
for ( ii in 1:length(Significant_in_GSEA_not_in_dcor) ){
aux_genes <- intersect(pathway_collapsed[[Significant_in_GSEA_not_in_dcor[[ii]]]],colnames(expressions))
if ( identical(aux_genes, character(0))) next
aux_pathway_dcor <- dcor.test(dist(expressions[,aux_genes]),dist(genotypes),R=10000)
aux_individual_genes_in_pathway_dcor <- sapply(aux_genes,function(x) dcor.test(dist(expressions[,x]),dist(genotypes),R=10000)$p.value<0.05 )
aux_enrichment_ratio_dcor <- sum(aux_individual_genes_in_pathway_dcor)/length(aux_individual_genes_in_pathway_dcor)
enrichment_ratio_dcor[ii] <- aux_enrichment_ratio_dcor

aux_individual_genes_in_pathway_ttest <- sapply(aux_genes,function(x) t.test(expressions[,x]~genotypes)$p.value<0.05 )
aux_enrichment_ratio_ttest <- sum(aux_individual_genes_in_pathway_ttest)/length(aux_individual_genes_in_pathway_ttest)
aux_enrichment_ratio_ttest
enrichment_ratio_ttest[ii] <-aux_enrichment_ratio_ttest
}


enrichment_ratio_comparison <- rbind(enrichment_ratio_dcor,enrichment_ratio_ttest)
rownames(enrichment_ratio_comparison) <- c("MPEA","GSEA")
colnames(enrichment_ratio_comparison) <- Significant_in_GSEA_not_in_dcor

enrichment_ratio_comparison%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
LUI_TARGETS_OF_PAX8_PPARG_FUSION LUI_THYROID_CANCER_CLUSTER_3 ANDERSEN_LIVER_CANCER_KRT19_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN MCBRYAN_PUBERTAL_BREAST_3_4WK_DN REACTOME_INFLUENZA_LIFE_CYCLE LANDIS_ERBB2_BREAST_TUMORS_324_UP KEGG_ALZHEIMERS_DISEASE REACTOME_METABOLISM_OF_RNA CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP REACTOME_RESPIRATORY_ELECTRON_TRANSPORT FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY REACTOME_METABOLISM_OF_MRNA PECE_MAMMARY_STEM_CELL_UP KEGG_NUCLEOTIDE_EXCISION_REPAIR TONG_INTERACT_WITH_PTTG1 EHLERS_ANEUPLOIDY_UP YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP KANNAN_TP53_TARGETS_DN DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX REACTOME_TRANSLATION REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES TAKAO_RESPONSE_TO_UVB_RADIATION_UP BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE HUMMERICH_BENIGN_SKIN_TUMOR_UP HSIAO_HOUSEKEEPING_GENES JAZAG_TGFB1_SIGNALING_UP BAE_BRCA1_TARGETS_UP KEGG_RIBOSOME NUTT_GBM_VS_AO_GLIOMA_DN MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN REACTOME_METABOLISM_OF_PROTEINS BILANGES_SERUM_RESPONSE_TRANSLATION LANDIS_BREAST_CANCER_PROGRESSION_UP NAKAYAMA_FGF2_TARGETS HUNSBERGER_EXERCISE_REGULATED_GENES LUI_THYROID_CANCER_PAX8_PPARG_DN WENG_POR_TARGETS_GLOBAL_UP REACTOME_PEPTIDE_CHAIN_ELONGATION NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON IRITANI_MAD1_TARGETS_DN YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 LEE_LIVER_CANCER_SURVIVAL_DN REACTOME_SIGNAL_AMPLIFICATION WANG_RESPONSE_TO_FORSKOLIN_UP JIANG_AGING_HYPOTHALAMUS_UP PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP KEGG_BASAL_TRANSCRIPTION_FACTORS OSMAN_BLADDER_CANCER_DN YANG_BREAST_CANCER_ESR1_UP ZHAN_MULTIPLE_MYELOMA_HP_UP PARK_HSC_MARKERS REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS WANG_TUMOR_INVASIVENESS_UP REACTOME_GLOBAL_GENOMIC_NER_GG_NER GEORGES_CELL_CYCLE_MIR192_TARGETS MAINA_VHL_TARGETS_DN CHEN_PDGF_TARGETS SCHRAMM_INHBA_TARGETS_DN FAELT_B_CLL_WITH_VH3_21_DN BOUDOUKHA_BOUND_BY_IGF2BP2 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN MURAKAMI_UV_RESPONSE_1HR_UP PID_PI3K_PLC_TRK_PATHWAY REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP CHANGOLKAR_H2AFY_TARGETS_UP BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN BORLAK_LIVER_CANCER_EGF_UP REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 KIM_MYC_AMPLIFICATION_TARGETS_UP LINDGREN_BLADDER_CANCER_CLUSTER_1_UP CHANGOLKAR_H2AFY_TARGETS_DN HORIUCHI_WTAP_TARGETS_DN SASAKI_ADULT_T_CELL_LEUKEMIA GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN REACTOME_INTEGRATION_OF_ENERGY_METABOLISM DELASERNA_MYOD_TARGETS_UP KASLER_HDAC7_TARGETS_2_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN SHIN_B_CELL_LYMPHOMA_CLUSTER_8 DOANE_BREAST_CANCER_ESR1_DN BIOCARTA_AGR_PATHWAY REACTOME_RNA_POL_I_PROMOTER_OPENING REACTOME_HDL_MEDIATED_LIPID_TRANSPORT FAELT_B_CLL_WITH_VH3_21_UP KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 HASLINGER_B_CLL_WITH_6Q21_DELETION KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN KEGG_PPAR_SIGNALING_PATHWAY REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE MIKKELSEN_MEF_LCP_WITH_H3K27ME3 XU_GH1_EXOGENOUS_TARGETS_DN ABE_VEGFA_TARGETS_2HR FIGUEROA_AML_METHYLATION_CLUSTER_1_DN REACTOME_LIPOPROTEIN_METABOLISM BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN BIOCARTA_UCALPAIN_PATHWAY ST_T_CELL_SIGNAL_TRANSDUCTION DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY HUMMERICH_MALIGNANT_SKIN_TUMOR_DN CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP PID_NCADHERIN_PATHWAY HUMMERICH_BENIGN_SKIN_TUMOR_DN REACTOME_PACKAGING_OF_TELOMERE_ENDS LEI_HOXC8_TARGETS_DN PID_BARD1_PATHWAY FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP BIOCARTA_MAL_PATHWAY XU_AKT1_TARGETS_6HR PID_INSULIN_GLUCOSE_PATHWAY REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS SA_B_CELL_RECEPTOR_COMPLEXES SCHEIDEREIT_IKK_INTERACTING_PROTEINS REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP RIZ_ERYTHROID_DIFFERENTIATION_HEMGN MEISSNER_BRAIN_HCP_WITH_H3K27ME3 REACTOME_SEMAPHORIN_INTERACTIONS KUMAR_AUTOPHAGY_NETWORK SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN KENNY_CTNNB1_TARGETS_UP OXFORD_RALA_OR_RALB_TARGETS_UP LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP MIKKELSEN_NPC_HCP_WITH_H3K27ME3 BIOCARTA_HER2_PATHWAY FIGUEROA_AML_METHYLATION_CLUSTER_3_DN KYNG_DNA_DAMAGE_BY_4NQO MULLIGHAN_NPM1_SIGNATURE_3_DN PID_IL23_PATHWAY REACTOME_MEIOTIC_RECOMBINATION MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP QI_HYPOXIA
MPEA 0.0417 0.0000 0.0714 0.1972 0.0732 0.1290 0.0630 0.0467 0.1250 0.0509 0.0682 0.1636 0.0556 0 0.0546 0.0721 0.0476 0.1379 0.069 0.0222 0.0000 0.0000 0.2105 0.0625 0.0565 0.0625 0.0400 0.0833 0.0707 0.0000 0.0557 0.0549 0.0303 0.0732 0.0571 0.1404 0 0.0500 0.0385 0 0.0952 0.0333 0.0000 0 0.0741 0.0606 0.0323 0.0687 0.0703 0.04 0.0667 0.100 0 0.0000 0.0333 0.0490 0.0000 0.0294 0.0312 0.0435 0.0463 0.0625 0.08 0.0625 0 0 0.05 0.0811 0.0435 0.0538 0.0625 0.2667 0 0.0 0.0444 0.0455 0.0417 0.0714 0.0962 0.0811 0.0182 0.0758 0.0610 0.0769 0.0481 0.0470 0.0525 0.0737 0.0423 0.0476 0.0556 0.0645 0.0909 0.1515 0.0233 0.3333 0.0556 0.0588 0.0588 0.0617 0.0508 0.0270 0.0000 0.0125 0 0.0741 0.2500 0 0.1333 0.0698 0.08 0.1333 0.0345 0.0323 0.125 0.0294 0 0.0385 0.1111 0.0556 0.0476 0.1739 0.0625 0.0000 0 0.0833 0.0484 0 0.04 0.0244 0.0862 0.0732 0.1250 0.0682 0.1053 0.0215 0.0464 0.0455 0.0000 0.0645 0.0382 0.0000 0.0156 0.0345 0.0957 0.0495
GSEA 0.0833 0.0526 0.1071 0.1408 0.0732 0.0968 0.0787 0.0467 0.1103 0.0602 0.0682 0.1273 0.1111 0 0.0656 0.0631 0.0714 0.1379 0.069 0.0444 0.0526 0.0625 0.1579 0.0833 0.0726 0.0625 0.0267 0.1250 0.0909 0.0667 0.0645 0.0549 0.0303 0.0976 0.0571 0.0702 0 0.0533 0.0385 0 0.1429 0.0667 0.0312 0 0.0988 0.0606 0.0323 0.0611 0.0625 0.12 0.0667 0.125 0 0.0667 0.0667 0.0571 0.0303 0.0294 0.0312 0.0000 0.0320 0.0625 0.08 0.0000 0 0 0.05 0.0946 0.0652 0.0538 0.0417 0.2000 0 0.1 0.0222 0.0000 0.0833 0.0476 0.0769 0.0541 0.0364 0.0833 0.0854 0.1154 0.0385 0.0201 0.0612 0.0526 0.0282 0.0476 0.0000 0.0645 0.0682 0.1515 0.0465 0.3333 0.1111 0.0588 0.0588 0.0741 0.0678 0.0541 0.0294 0.0250 0 0.1111 0.2083 0 0.1333 0.0698 0.08 0.1333 0.0345 0.0323 0.125 0.0588 0 0.0385 0.0556 0.0556 0.0476 0.1304 0.0625 0.0833 0 0.0833 0.0806 0 0.00 0.0427 0.0862 0.0732 0.2083 0.0682 0.1053 0.0323 0.0515 0.0455 0.0435 0.0968 0.0534 0.0625 0.0312 0.0383 0.0696 0.0396 
t.test(enrichment_ratio_dcor,enrichment_ratio_ttest)
## 
##  Welch Two Sample t-test
## 
## data:  enrichment_ratio_dcor and enrichment_ratio_ttest
## t = -1.0208, df = 287.16, p-value = 0.3082
## alternative hypothesis: true difference in means is not equal to 0
## 95 percent confidence interval:
##  -0.017581364  0.005572975
## sample estimates:
##  mean of x  mean of y 
## 0.05955527 0.06555946
enrichment_ratios_percenages <- rbind(sum(enrichment_ratio_dcor>enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor<enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor),
sum(enrichment_ratio_dcor==enrichment_ratio_ttest,na.rm = T)/length(enrichment_ratio_dcor))*100
rownames(enrichment_ratios_percenages) <- c ( "More univariate enrichment detected in Dcor", "More univariate enrichment detected in T-test", "Draw" )
colnames(enrichment_ratios_percenages) <- "Percentage"

enrichment_ratios_percenages%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
Percentage
More univariate enrichment detected in Dcor 21.9178
More univariate enrichment detected in T-test 40.4110
Draw 37.6712

Close cluster

# stopCluster(cl)

PCA plot of pathways deemed significant in MPEA but not GSEA

library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 

# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP"

## [1] "AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN"

## [1] "AMIT_EGF_RESPONSE_40_MCF10A"

## [1] "BASAKI_YBX1_TARGETS_UP"

## [1] "BERNARD_PPAPDC1B_TARGETS_UP"

## [1] "BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN"

## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"

## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"

## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"

## [1] "BIOCARTA_CARDIACEGF_PATHWAY"

## [1] "BIOCARTA_CDC42RAC_PATHWAY"

## [1] "BIOCARTA_EDG1_PATHWAY"

## [1] "BIOCARTA_P53HYPOXIA_PATHWAY"

## [1] "BIOCARTA_PAR1_PATHWAY"

## [1] "BIOCARTA_PTDINS_PATHWAY"

## [1] "BIOCARTA_RACCYCD_PATHWAY"

## [1] "BIOCARTA_RAS_PATHWAY"

## [1] "BOCHKIS_FOXA2_TARGETS"

## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_UP"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN"

## [1] "BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP"

## [1] "BROWNE_HCMV_INFECTION_48HR_UP"

## [1] "BROWNE_HCMV_INFECTION_4HR_DN"

## [1] "BROWNE_HCMV_INFECTION_6HR_DN"

## [1] "BRUECKNER_TARGETS_OF_MIRLET7A3_UP"

## [1] "BURTON_ADIPOGENESIS_6"

## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN"

## [1] "BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS"

## [1] "CADWELL_ATG16L1_TARGETS_DN"

## [1] "CAFFAREL_RESPONSE_TO_THC_DN"

## [1] "CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP"

## [1] "CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP"

## [1] "CHEBOTAEV_GR_TARGETS_DN"

## [1] "CHEN_ETV5_TARGETS_TESTIS"

## [1] "COATES_MACROPHAGE_M1_VS_M2_DN"

## [1] "COATES_MACROPHAGE_M1_VS_M2_UP"

## [1] "CUI_GLUCOSE_DEPRIVATION"

## [1] "CUI_TCF21_TARGETS_DN"

## [1] "DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP"

## [1] "DAZARD_RESPONSE_TO_UV_NHEK_DN"

## [1] "DE_YY1_TARGETS_UP"

## [1] "DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN"

## [1] "DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER"

## [1] "ENGELMANN_CANCER_PROGENITORS_DN"

## [1] "ENK_UV_RESPONSE_KERATINOCYTE_DN"

## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_BASAL"

## [1] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"

## [1] "FISCHER_DIRECT_P53_TARGETS_META_ANALYSIS"

## [1] "FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN"

## [1] "FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP"

## [1] "FORTSCHEGGER_PHF8_TARGETS_UP"

## [1] "FOSTER_TOLERANT_MACROPHAGE_UP"

## [1] "FRIDMAN_IMMORTALIZATION_DN"

## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"

## [1] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"

## [1] "GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN"

## [1] "GARY_CD5_TARGETS_DN"

## [1] "GEISS_RESPONSE_TO_DSRNA_DN"

## [1] "GENTILE_UV_LOW_DOSE_UP"

## [1] "GEORGES_TARGETS_OF_MIR192_AND_MIR215"

## [1] "GOLUB_ALL_VS_AML_DN"

## [1] "GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN"

## [1] "GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP"

## [1] "GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN"

## [1] "GUILLAUMOND_KLF10_TARGETS_DN"

## [1] "GUTIERREZ_MULTIPLE_MYELOMA_UP"

## [1] "HASLINGER_B_CLL_WITH_MUTATED_VH_GENES"

## [1] "HEIDENBLAD_AMPLICON_12P11_12_UP"

## [1] "HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS"

## [1] "HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN"

## [1] "HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN"

## [1] "HORTON_SREBF_TARGETS"

## [1] "HOUSTIS_ROS"

## [1] "HU_ANGIOGENESIS_DN"

## [1] "HUANG_GATA2_TARGETS_UP"

## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN"

## [1] "IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP"

## [1] "JAEGER_METASTASIS_DN"

## [1] "JOHNSTONE_PARVB_TARGETS_3_UP"

## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"

## [1] "KASLER_HDAC7_TARGETS_1_DN"

## [1] "KEEN_RESPONSE_TO_ROSIGLITAZONE_UP"

## [1] "KEGG_PYRIMIDINE_METABOLISM"

## [1] "KEGG_RNA_POLYMERASE"

## [1] "KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT"

## [1] "KEGG_STEROID_BIOSYNTHESIS"

## [1] "KENNY_CTNNB1_TARGETS_DN"

## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"

## [1] "LABBE_WNT3A_TARGETS_DN"

## [1] "LAMB_CCND1_TARGETS"

## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"

## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"

## [1] "LEIN_CHOROID_PLEXUS_MARKERS"

## [1] "LENAOUR_DENDRITIC_CELL_MATURATION_DN"

## [1] "LI_INDUCED_T_TO_NATURAL_KILLER_DN"

## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"

## [1] "LIN_NPAS4_TARGETS_UP"

## [1] "LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q"

## [1] "LIU_PROSTATE_CANCER_UP"

## [1] "LIU_SOX4_TARGETS_UP"

## [1] "MA_MYELOID_DIFFERENTIATION_DN"

## [1] "MACLACHLAN_BRCA1_TARGETS_UP"

## [1] "MANALO_HYPOXIA_DN"

## [1] "MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5"

## [1] "MARKS_HDAC_TARGETS_UP"

## [1] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"

## [1] "MASSARWEH_RESPONSE_TO_ESTRADIOL"

## [1] "MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN"

## [1] "MCCLUNG_COCAINE_REWARD_5D"

## [1] "MENSE_HYPOXIA_UP"

## [1] "MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED"

## [1] "MISSIAGLIA_REGULATED_BY_METHYLATION_UP"

## [1] "MITSIADES_RESPONSE_TO_APLIDIN_UP"

## [1] "MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN"

## [1] "MOREIRA_RESPONSE_TO_TSA_UP"

## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_UP"

## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP"

## [1] "MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP"

## [1] "MULLIGHAN_NPM1_SIGNATURE_3_UP"

## [1] "MURAKAMI_UV_RESPONSE_24HR"

## [1] "MURAKAMI_UV_RESPONSE_6HR_DN"

## [1] "NADLER_HYPERGLYCEMIA_AT_OBESITY"

## [1] "NAGASHIMA_NRG1_SIGNALING_DN"

## [1] "NOJIMA_SFRP2_TARGETS_UP"

## [1] "NUYTTEN_NIPP1_TARGETS_UP"

## [1] "ODONNELL_METASTASIS_DN"

## [1] "ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP"

## [1] "OISHI_CHOLANGIOMA_STEM_CELL_LIKE_DN"

## [1] "ONDER_CDH1_TARGETS_1_UP"

## [1] "OUILLETTE_CLL_13Q14_DELETION_DN"

## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"

## [1] "PENG_RAPAMYCIN_RESPONSE_UP"

## [1] "PETRETTO_CARDIAC_HYPERTROPHY"

## [1] "PETRETTO_HEART_MASS_QTL_CIS_DN"

## [1] "PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP"

## [1] "PETROVA_PROX1_TARGETS_UP"

## [1] "PID_AVB3_INTEGRIN_PATHWAY"

## [1] "PID_ECADHERIN_KERATINOCYTE_PATHWAY"

## [1] "PID_ECADHERIN_NASCENT_AJ_PATHWAY"

## [1] "PID_EPHA_FWDPATHWAY"

## [1] "PID_EPHA2_FWD_PATHWAY"

## [1] "PID_IL4_2PATHWAY"

## [1] "PID_LIS1_PATHWAY"

## [1] "PID_P53_REGULATION_PATHWAY"

## [1] "PID_PRL_SIGNALING_EVENTS_PATHWAY"

## [1] "PID_PTP1B_PATHWAY"

## [1] "PID_S1P_S1P1_PATHWAY"

## [1] "PID_S1P_S1P2_PATHWAY"

## [1] "PID_S1P_S1P3_PATHWAY"

## [1] "PID_SYNDECAN_4_PATHWAY"

## [1] "PID_TGFBR_PATHWAY"

## [1] "PID_WNT_NONCANONICAL_PATHWAY"

## [1] "PLASARI_NFIC_TARGETS_BASAL_UP"

## [1] "PLASARI_TGFB1_TARGETS_10HR_DN"

## [1] "PUJANA_BRCA2_PCC_NETWORK"

## [1] "QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2"

## [1] "RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP"

## [1] "RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN"

## [1] "REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT"

## [1] "REACTOME_CHOLESTEROL_BIOSYNTHESIS"

## [1] "REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX"

## [1] "REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX"

## [1] "REACTOME_G_ALPHA1213_SIGNALLING_EVENTS"

## [1] "REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA"

## [1] "REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING"

## [1] "REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE"

## [1] "REACTOME_MICRORNA_MIRNA_BIOGENESIS"

## [1] "REACTOME_MRNA_SPLICING_MINOR_PATHWAY"

## [1] "REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING"

## [1] "REACTOME_PEROXISOMAL_LIPID_METABOLISM"

## [1] "REACTOME_PI3K_AKT_ACTIVATION"

## [1] "REACTOME_REGULATORY_RNA_PATHWAYS"

## [1] "REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER"

## [1] "REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION"

## [1] "REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING"

## [1] "REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE"

## [1] "RICKMAN_METASTASIS_UP"

## [1] "RIGGI_EWING_SARCOMA_PROGENITOR_DN"

## [1] "RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP"

## [1] "RODWELL_AGING_KIDNEY_NO_BLOOD_DN"

## [1] "ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP"

## [1] "SA_TRKA_RECEPTOR"

## [1] "SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN"

## [1] "SANSOM_APC_TARGETS_DN"

## [1] "SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1"

## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP"

## [1] "SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP"

## [1] "SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP"

## [1] "SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY"

## [1] "SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP"

## [1] "SHEN_SMARCA2_TARGETS_UP"

## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"

## [1] "SHI_SPARC_TARGETS_UP"

## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN"

## [1] "SMITH_TERT_TARGETS_DN"

## [1] "TARTE_PLASMA_CELL_VS_PLASMABLAST_DN"

## [1] "TERAMOTO_OPN_TARGETS_CLUSTER_7"

## [1] "TIAN_TNF_SIGNALING_NOT_VIA_NFKB"

## [1] "TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP"

## [1] "UEDA_PERIFERAL_CLOCK"

## [1] "VANTVEER_BREAST_CANCER_ESR1_UP"

## [1] "VARELA_ZMPSTE24_TARGETS_UP"

## [1] "VERHAAK_GLIOBLASTOMA_NEURAL"

## [1] "VERRECCHIA_EARLY_RESPONSE_TO_TGFB1"

## [1] "WALLACE_PROSTATE_CANCER_RACE_UP"

## [1] "WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP"

## [1] "WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN"

## [1] "WANG_SMARCE1_TARGETS_UP"

## [1] "WANG_TARGETS_OF_MLL_CBP_FUSION_DN"

## [1] "WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP"

## [1] "WHITFIELD_CELL_CYCLE_G2"

## [1] "WIERENGA_STAT5A_TARGETS_GROUP1"

## [1] "WIERENGA_STAT5A_TARGETS_GROUP2"

## [1] "WIERENGA_STAT5A_TARGETS_UP"

## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"

## [1] "WINZEN_DEGRADED_VIA_KHSRP"

## [1] "YAGI_AML_RELAPSE_PROGNOSIS"

## [1] "YAGI_AML_WITH_T_8_21_TRANSLOCATION"

## [1] "YAMASHITA_METHYLATED_IN_PROSTATE_CANCER"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5"

## [1] "ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN"

## [1] "ZHANG_TLX_TARGETS_60HR_DN"

## [1] "ZHENG_FOXP3_TARGETS_IN_THYMUS_UP"

PCA plot of pathways deemed significant in GSEA but not MPEA

# rownames(gsea_results_significant)
# for (name in (Significant_in_GSEA_not_in_dcor)){
#   strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
#   expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
#   genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
#   genotypes_category <- as.data.frame(genotypes_category)
#   print(name)
#   print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 
#   
#   # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
#   # biplot.pcoa(pcoa.obj)
# }